Gpiv

Gpiv is a graphic user interface program for recording and analyzing images obtained from a fluid flow that has been seeded with tracer particles by the so-called Particle Image Velocimetry technique (PIV). The program allows to have a quick overview of the parameter settings of all processes, easily changing them, executing the processes and visualizing their results in an interactive way.
Find Gpiv at: http://gpiv.sourceforge.net/

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AMBER

AMBER is group of programs used for simulation of biomolecules. It is highly efficient parallel MD simulation program written in FORTRAN.
Find AMBER at: http://ambermd.org/

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New Software Links

We’ve been completely swamped lately with duties relating to Freshman chemistry. There’s been a backlog of new OpenSource scientific software, so without further ado:

In our Partial Differential Equation section, we’ve got a new link to FEniCS, which appears to be a super-project that has a bunch of smaller packages for dealing with finite element simulations.

Our Mathematics section has a new link to Lybniz, a general purpose function grapher.

Madagascar is the latest entry in our Geology and Geophysics section. It looks to be a new geophysical data processing tool written completely fresh from the ground up!

Our Algorithms and Computational Theory section gets a new link to oMetah, or “Open Metaheuristics,” a set of tools for genetic/evolutionnary algorithms, tabu searches, simulated annealing, ant colony algorithms, etc. It looks good for hard mono-objective continuous optimization problems.

Debyer takes a file with atom positions as input and can output X-ray and neutron diffraction patterns, the total scattering structure function, the pair distribution function (PDF), and related functions (RDF, reduced PDF). It can be used for comparison of molecular dynamics simulations or other models of atomistic structure of the material with X-ray and neutron powder diffraction experiments. It makes an appearance in our Crystallography section.

I wasn’t sure how to categorize SwisTrak. It allows for tracking multiple objects such as insects or robots from a video stream provided by a file or directly from a camera. Where does it belong? Life Sciences? Engineering? Both!

Our Mathematics Education section gets an entry for NA_WorkSheet, a Java-based worksheet that contains a whole bunch of numerical analysis tools.

And finally, Gretl now appears in our Statistics section. Gretl is a package for econometric analysis, written in C.

Keep those links coming!

[tags]Open source, Science, Software[/tags]

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Posted in Science, Software | 4 Comments

Engineering Science Blog

Our friends Geoff Davis and Peter Fiske over at PhDs.org have started a new blog called Engineering Science. The first few posts have been very good, including these excellent posts on writing effective grant proposals and the stereotype threat.

Go check it out!

[tags]engineering, science, grantsmanship, careers[/tags]

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Posted in education, Policy, Science | 1 Comment

Gretl

Gretl (Gnu Regression, Econometrics and Time-series Library) is a cross-platform software package for econometric analysis, written in the C programming language. It is is free, open-source software. You may redistribute it and/or modify it under the terms of the GNU General Public License (GPL).
Find Gretl at: http://gretl.sf.net

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NA_WorkSheet

The NA_WorkSheet is a collective aggregation of algorithms coded in Java that implements various Numerical Analysis solutions/techniques in one easy to use opensource tool. The app. may be used for graphing, root finding, differentiation, integration, interpolation, linear systems solving, and matrix operations.
Find NA_WorkSheet at: http://na-worksheet.sourceforge.net/

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Scientific Expert or Not. Does it matter?

Slate Magazine is running an article about a Sociologist who posed as a physicist. Harry Collins (the sociologist) studies “expertise” in his day job, but has a strong interest in experiments for detecting gravitational waves. He and his colleagues collected a set of lay questions about gravitational wave detectors. They got an expert in the field to answer them, and Collins himself wrote his own set of answers. Both sets of answers were submitted to a group of nine experts in gravitational waves as a mini Turing test to figure out “which is the real physicist”. Seven of the nine picked Collins’ answers. The paper describing the experiment is here

Slate is trying to sell this experiment as the inverse of Alan Sokal’s famous hack on the post-modern journal, Social Text. But it isn’t. Not a single scientist is going to be surprised that a talented and interested amateur can understand their field well enough to answer qualitative questions about it. Science is not a secret society, and our methods and results are open to the public. Smart people without formal training can talk intelligently about science, they can get published in the journals if they write a good enough paper and they can often write better than the experts.

The only exception would be if a field requires specific kinds of mathematical training, but even then, amateurs can develop this expertise on their own and scientists will have few problems interacting with them. I’d argue that Collins has made himself nearly the equivalent of a practicing researcher in gravitational waves. He certainly learned enough to make himself something of a science writer. (Actually his answers are pleasingly light in technical jargon.) Good for him, but it still doesn’t say anything about exclusionary practices in science.

In fact, in thinking it through, I’m not sure I see the point. Perhaps the Slate article is spinning it a bit too much…

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Posted in education, Science | 7 Comments

SwisTrack: Multi-Object Video Tracking Software

SwisTrack allows for tracking multiple objects such as insects or robots from a video stream provided by a file or directly from a camera. SwisTrack’s user interface allows adjusting parameters on the flight, and thus allow to find an optimal tracking configuration choosing from a suite of already implemented algorithms for segmentation and filtering in an intuitive fashion. Contributing code to SwisTrack is made easy as tracking core and GUI share an XML description of available tracking modes and its parameters.
Find SwisTrack: Multi-Object Video Tracking Software at: http://swistrack.sourceforge.net

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I saw the best minds of my generation destroyed by Google

Here’s an amazing rant / short story from Bruce Sterling called “I saw the best minds of my generation destroyed by Google”. Any story that obliquely references to Steve Jobs and The Smiths can’t be bad…

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Debyer

Debyer and companion programs analyze and manipulate atomistic models. In particular, debyer can calculate powder diffraction pattern of virtual sample using the Debye scattering formula. It takes as an input a file with positions of all the atoms in the virtual sample (up to tens of millions of atoms, perhaps even more) and can output x-ray and neutron powder diffraction pattern, total scattering structure function, pair distribution/correlation function (PDF/PCF) and related functions (RDF, reduced PDF).
Find Debyer at: https://github.com/wojdyr/debyer

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Posted in Crystallography | Leave a comment